Simple examples¶
Install a genome¶
Any genome on UCSC, Ensembl or NCBI can be installed automatically using genomepy. The genomepy
command tool comes installed with gimmemotifs. For instance, to download the hg38 genome from UCSC:
$ genomepy install hg38 UCSC --annotation
Predict de novo motifs¶
For a quick analysis, to see if it works:
$ gimme motifs TAp73alpha.bed -g hg19 -n gimme.p73 -a small -t Homer,MDmodule,BioProspector
For a full analysis:
$ gimme motifs TAp73alpha.bed -g hg19 -n gimme.p73
Open the file gimme.p73/gimme.denovo.html
in your web browser to see the results.
Compare motifs between data sets¶
$ gimme maelstrom hg19.blood.most_variable.1k.txt hg19 maelstrom.out/
The output scores of gimme maelstrom
represent the combined result of multiple methods.
The individual results from different methods are ranked from high-scoring motif to low-scoring motif and converted
to z-scores using the inverse normal transformation. The z-scores from individual methods are then combined using
Stouffer’s method. The score that is shown is the aggregated z-score. A higher z-score means that presence of
the motif or a higher motif score is associated with higher signal in a specific sample.
Create sequence logos¶
$ gimme logo -i GM.5.0.p53.0004
This will generate GM.5.0.p53.0004.png
.
Use the -p
argument for a different pwm file.
The following command will generate a logo for every motif in custom.pfm
.
$ gimme logo -p custom.pfm